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Mladen Vujosevic - One of the best experts on this subject based on the ideXlab platform.

  • host B Chromosomes as potential sex ratio distorters of intestinal nematode infrapopulations in the yellow necked mouse apodemus flavicollis
    Journal of Helminthology, 2019
    Co-Authors: Vladimir M Jovanovic, Jelena Blagojevic, Borislav Cabrilo, Olivera Bjeliccabrilo, Ivana Budinski, Tanja Adnađevic, Mladen Vujosevic
    Abstract:

    The yellow-necked mouse, Apodemus flavicollis, can Be considered as a model for genetic polymorphism produced By the frequent presence of supernumerary or B Chromosomes (Bs). Host genetic Background is rarely taken into account in studies of parasite sex ratio. The main aim of this study was to investigate the range of infrapopulation sex ratios for nematode parasites of the yellow-necked mouse and to determine which factors most influence variation in parasite sex ratios. Six nematode species found in the collected yellow-necked mice were analysed. We confirmed the predominant pattern of female-Biased sex ratios in verteBrate parasite infrapopulations. The presence of B Chromosomes in host genomes played an important role in infrapopulations of Heligmosomoides polygyrus, Syphacia stroma and Trichuris muris, as hosts with B Chromosomes carried a higher proportion of males. The relative increase of males in infrapopulations could result from a shift in parasite life history strategy, induced By adaptation to the specific host genotypes (Bs present). In a meta-analysis with previously puBlished data, the sex determination system was demonstrated to play a significant role in nematode sex ratio variation, as well as specific life history patterns, such as the place of egg hatching.

  • Low-pass single-chromosome sequencing of human small supernumerary marker Chromosomes (sSMCs) and Apodemus B Chromosomes
    Chromosoma, 2018
    Co-Authors: Alexey I. Makunin, Marija Rajičić, Tatyana V. Karamysheva, Svetlana A. Romanenko, Anna S. Druzhkova, Nikolay B. Rubtsov, Alexander S. Graphodatsky, Mladen Vujosevic, Jelena Blagojevic, Vladimir A. Trifonov
    Abstract:

    Supernumerary Chromosomes sporadically arise in many eukaryotic species as a result of genomic rearrangements. If present in a suBstantial part of species population, those are called B Chromosomes, or Bs. This is the case for 70 mammalian species, most of which are rodents. In humans, the most common types of extra Chromosomes, sSMCs (small supernumerary marker Chromosomes), are diagnosed in approximately 1 of 2000 postnatal cases. Due to low frequency in population, human sSMCs are not considered B Chromosomes. Genetic content of Both B-Chromosomes and sSMCs in most cases remains understudied. Here, we apply microdissection of single Chromosomes with suBsequent low-pass sequencing on Ion Torrent PGM and Illumina MiSeq to identify unique and repetitive DNA sequences present in a single human sSMC and several B Chromosomes in mice Apodemus flavicollis and Apodemus peninsulae . The pipeline for sequencing data analysis was made availaBle in Galaxy interface as an addition to previously puBlished command-line version. Human sSMC was attriButed to the proximal part of chromosome 15 long arm, and Breakpoints leading to its formation were located into satellite DNA arrays. Genetic content of Apodemus B Chromosomes was species-specific, and minor alterations were oBserved in Both species. Common features of Bs in these Apodemus species were satellite DNA and ERV enrichment, as well as the presence of the vaccinia-related kinase gene Vrk1 . Understanding of the non-essential genome elements content provides important insights into genome evolution in general.

  • the origin of B Chromosomes in yellow necked mice apodemus flavicollis Break rules But keep playing the game
    PLOS ONE, 2017
    Co-Authors: Marija Rajicic, Tatyana V. Karamysheva, Svetlana A. Romanenko, Vladimir A. Trifonov, Jelena Blagojevic, Ivana Budinski, Tanja Adnađevic, A S Bogdanov, N B Rubtsov, Mladen Vujosevic
    Abstract:

    B Chromosomes (Bs) are known for more than hundred years But their origin, structure and pattern of evolution are not well understood. In the past few years new methodological approaches, involving isolation of Bs followed By whole DNA amplification, DNA proBe generation, and fluorescent in situ hyBridization (FISH) or the B chromosome DNA sequencing, has allowed detailed analysis of their origin and molecular structure in different species. In this study we explored the origin of Bs in the yellow-necked wood mouse, Apodemus flavicollis, using generation of microdissected DNA proBes followed By FISH on metaphase Chromosomes. Bs of A. flavicollis were successfully isolated and DNA was used as the template for B-specific proBes for the first time. We revealed homology of DNA derived from the analyzed B Chromosomes to the pericentromeric region (PR) of sex Chromosomes and suBtelomeric region of two pairs of small autosomes, But lower homology to the rest of the Y chromosome. Moreover, all analysed Bs had the same structure regardless of their numBer per individual or the great geographic distance Between examined populations from the Balkan Peninsula (SerBia) and Eastern Europe (south region of Russia and central Belarus). Therefore, it was suggested that B Chromosomes in A. flavicollis have a unique common origin from the PR of sex Chromosomes, and/or similar evolutionary pattern.

  • exploring supernumeraries a new marker for screening of B Chromosomes presence in the yellow necked mouse apodemus flavicollis
    PLOS ONE, 2016
    Co-Authors: Vanja Bugarskistanojevic, Jelena Blagojevic, Marija Rajicic, Gorana Stamenkovic, Thomas Liehr, Nadezda Kosyakova, Mladen Vujosevic
    Abstract:

    Since the density of simple sequence repeats (SSRs) may vary Between different Chromosomes of the same species in eukaryotic genomes, we screened SSRs of the whole genome of the yellow necked mouse, Apodemus flavicollis, in order to reveal SSR profiles specific for animals carrying B Chromosomes. We found that the 2200 Bp Band was amplified By primer (CAG)4AC to a highly increased level in samples with B Chromosomes. This quantitative difference (B-marker) Between animals with (+B) and without (0B) B Chromosomes was used to screen 20 populations (387 animals). The presence/aBsence of Bs was confirmed in 96.5% of 342 non mosaic individuals, which recommends this method for noninvasive B-presence detection. A group of 45 animals with mosaic and micro B (μB) karyotypes was considered separately and showed 55.6% of overall congruence Between karyotyping and molecular screening results. Relative quantification By qPCR of two different targeted sequences from B-marker indicated that these B-specific fragments are multiplied on B Chromosomes. It also confirms our assumption that different types of Bs with variaBle molecular composition may exist in the same individual and Between individuals of this species. Our results suBstantiate the origin of Bs from the standard chromosomal complement. The B-marker showed 98% sequence identity with the serine/threonine protein kinase VRK1 gene, similarly to findings reported for Bs from phylogenetically highly distant mammalian species. Evolutionarily conserved protein-coding genes found in Bs, including this one in A. flavicollis, could suggest a common evolutionary pathway.

  • screening of B Chromosomes for presence of two genes in yellow necked mice apodemus flavicollis mammalia rodentia
    Genetika, 2015
    Co-Authors: Marija Rajicic, Tanja Adnadjevic, Jelena Blagojevic, Gorana Stamenkovic, Mladen Vujosevic
    Abstract:

    B Chromosomes (Bs) are a very heterogeneous group of extra Chromosomes. In various species Bs occur with different nucleotide sequences ranging from repetitive to protein coding. In yellow-necked field mice, Apodemus flavicollis Bs are small euchromatic Chromosomes and untill now, only few molecular analyses have Been conducted. In this study we examined A. flavicollis individuals with different numBer of Bs for presence of two genes, C-KIT and 18S rRNA. The C-KIT proto-oncogene was found on Bs in three Canidae species and one Cervidae species. This gene is a coding receptor critical for proliferation and cell differentiation of hematopoietic, melanoBlast and primordial germ cells, and is highly conserved within mammals. While using semiquantitative PCR, we did not notice any difference in the C-KIT Band intensity among animals with different numBer of Bs (0-3). The presence of only one copy of C- KIT gene was confirmed using real time-PCR on genomic DNA of A. flavicollis specimens with different numBer of Bs. rRNA genes in eukaryotes’ genome are organized like units of tandem repeated sequences. The units form distinct clusters on one to several chromosome pairs. rRNA genes were found on Bs in different species including two species of genus Apodemus. One particular sample with 2 Bs showed the numBer of 18S rRNA gene aBout three times that of the caliBrator 0 B sample. This result can indicate the presence of 18S rRNA gene on Bs, But its confirmation requires the implementation of other methods. Still, we can neither confirm nor deny the existence of pseudogen of tested target genes, or lose of exon 1 of C-KIT protooncogen in Bs of A. flavicollis. Our findings are further discussed. [Projekat Ministarstva nauke RepuBlike SrBije, Br. 173003]

Jelena Blagojevic - One of the best experts on this subject based on the ideXlab platform.

  • host B Chromosomes as potential sex ratio distorters of intestinal nematode infrapopulations in the yellow necked mouse apodemus flavicollis
    Journal of Helminthology, 2019
    Co-Authors: Vladimir M Jovanovic, Jelena Blagojevic, Borislav Cabrilo, Olivera Bjeliccabrilo, Ivana Budinski, Tanja Adnađevic, Mladen Vujosevic
    Abstract:

    The yellow-necked mouse, Apodemus flavicollis, can Be considered as a model for genetic polymorphism produced By the frequent presence of supernumerary or B Chromosomes (Bs). Host genetic Background is rarely taken into account in studies of parasite sex ratio. The main aim of this study was to investigate the range of infrapopulation sex ratios for nematode parasites of the yellow-necked mouse and to determine which factors most influence variation in parasite sex ratios. Six nematode species found in the collected yellow-necked mice were analysed. We confirmed the predominant pattern of female-Biased sex ratios in verteBrate parasite infrapopulations. The presence of B Chromosomes in host genomes played an important role in infrapopulations of Heligmosomoides polygyrus, Syphacia stroma and Trichuris muris, as hosts with B Chromosomes carried a higher proportion of males. The relative increase of males in infrapopulations could result from a shift in parasite life history strategy, induced By adaptation to the specific host genotypes (Bs present). In a meta-analysis with previously puBlished data, the sex determination system was demonstrated to play a significant role in nematode sex ratio variation, as well as specific life history patterns, such as the place of egg hatching.

  • Low-pass single-chromosome sequencing of human small supernumerary marker Chromosomes (sSMCs) and Apodemus B Chromosomes
    Chromosoma, 2018
    Co-Authors: Alexey I. Makunin, Marija Rajičić, Tatyana V. Karamysheva, Svetlana A. Romanenko, Anna S. Druzhkova, Nikolay B. Rubtsov, Alexander S. Graphodatsky, Mladen Vujosevic, Jelena Blagojevic, Vladimir A. Trifonov
    Abstract:

    Supernumerary Chromosomes sporadically arise in many eukaryotic species as a result of genomic rearrangements. If present in a suBstantial part of species population, those are called B Chromosomes, or Bs. This is the case for 70 mammalian species, most of which are rodents. In humans, the most common types of extra Chromosomes, sSMCs (small supernumerary marker Chromosomes), are diagnosed in approximately 1 of 2000 postnatal cases. Due to low frequency in population, human sSMCs are not considered B Chromosomes. Genetic content of Both B-Chromosomes and sSMCs in most cases remains understudied. Here, we apply microdissection of single Chromosomes with suBsequent low-pass sequencing on Ion Torrent PGM and Illumina MiSeq to identify unique and repetitive DNA sequences present in a single human sSMC and several B Chromosomes in mice Apodemus flavicollis and Apodemus peninsulae . The pipeline for sequencing data analysis was made availaBle in Galaxy interface as an addition to previously puBlished command-line version. Human sSMC was attriButed to the proximal part of chromosome 15 long arm, and Breakpoints leading to its formation were located into satellite DNA arrays. Genetic content of Apodemus B Chromosomes was species-specific, and minor alterations were oBserved in Both species. Common features of Bs in these Apodemus species were satellite DNA and ERV enrichment, as well as the presence of the vaccinia-related kinase gene Vrk1 . Understanding of the non-essential genome elements content provides important insights into genome evolution in general.

  • the origin of B Chromosomes in yellow necked mice apodemus flavicollis Break rules But keep playing the game
    PLOS ONE, 2017
    Co-Authors: Marija Rajicic, Tatyana V. Karamysheva, Svetlana A. Romanenko, Vladimir A. Trifonov, Jelena Blagojevic, Ivana Budinski, Tanja Adnađevic, A S Bogdanov, N B Rubtsov, Mladen Vujosevic
    Abstract:

    B Chromosomes (Bs) are known for more than hundred years But their origin, structure and pattern of evolution are not well understood. In the past few years new methodological approaches, involving isolation of Bs followed By whole DNA amplification, DNA proBe generation, and fluorescent in situ hyBridization (FISH) or the B chromosome DNA sequencing, has allowed detailed analysis of their origin and molecular structure in different species. In this study we explored the origin of Bs in the yellow-necked wood mouse, Apodemus flavicollis, using generation of microdissected DNA proBes followed By FISH on metaphase Chromosomes. Bs of A. flavicollis were successfully isolated and DNA was used as the template for B-specific proBes for the first time. We revealed homology of DNA derived from the analyzed B Chromosomes to the pericentromeric region (PR) of sex Chromosomes and suBtelomeric region of two pairs of small autosomes, But lower homology to the rest of the Y chromosome. Moreover, all analysed Bs had the same structure regardless of their numBer per individual or the great geographic distance Between examined populations from the Balkan Peninsula (SerBia) and Eastern Europe (south region of Russia and central Belarus). Therefore, it was suggested that B Chromosomes in A. flavicollis have a unique common origin from the PR of sex Chromosomes, and/or similar evolutionary pattern.

  • exploring supernumeraries a new marker for screening of B Chromosomes presence in the yellow necked mouse apodemus flavicollis
    PLOS ONE, 2016
    Co-Authors: Vanja Bugarskistanojevic, Jelena Blagojevic, Marija Rajicic, Gorana Stamenkovic, Thomas Liehr, Nadezda Kosyakova, Mladen Vujosevic
    Abstract:

    Since the density of simple sequence repeats (SSRs) may vary Between different Chromosomes of the same species in eukaryotic genomes, we screened SSRs of the whole genome of the yellow necked mouse, Apodemus flavicollis, in order to reveal SSR profiles specific for animals carrying B Chromosomes. We found that the 2200 Bp Band was amplified By primer (CAG)4AC to a highly increased level in samples with B Chromosomes. This quantitative difference (B-marker) Between animals with (+B) and without (0B) B Chromosomes was used to screen 20 populations (387 animals). The presence/aBsence of Bs was confirmed in 96.5% of 342 non mosaic individuals, which recommends this method for noninvasive B-presence detection. A group of 45 animals with mosaic and micro B (μB) karyotypes was considered separately and showed 55.6% of overall congruence Between karyotyping and molecular screening results. Relative quantification By qPCR of two different targeted sequences from B-marker indicated that these B-specific fragments are multiplied on B Chromosomes. It also confirms our assumption that different types of Bs with variaBle molecular composition may exist in the same individual and Between individuals of this species. Our results suBstantiate the origin of Bs from the standard chromosomal complement. The B-marker showed 98% sequence identity with the serine/threonine protein kinase VRK1 gene, similarly to findings reported for Bs from phylogenetically highly distant mammalian species. Evolutionarily conserved protein-coding genes found in Bs, including this one in A. flavicollis, could suggest a common evolutionary pathway.

  • screening of B Chromosomes for presence of two genes in yellow necked mice apodemus flavicollis mammalia rodentia
    Genetika, 2015
    Co-Authors: Marija Rajicic, Tanja Adnadjevic, Jelena Blagojevic, Gorana Stamenkovic, Mladen Vujosevic
    Abstract:

    B Chromosomes (Bs) are a very heterogeneous group of extra Chromosomes. In various species Bs occur with different nucleotide sequences ranging from repetitive to protein coding. In yellow-necked field mice, Apodemus flavicollis Bs are small euchromatic Chromosomes and untill now, only few molecular analyses have Been conducted. In this study we examined A. flavicollis individuals with different numBer of Bs for presence of two genes, C-KIT and 18S rRNA. The C-KIT proto-oncogene was found on Bs in three Canidae species and one Cervidae species. This gene is a coding receptor critical for proliferation and cell differentiation of hematopoietic, melanoBlast and primordial germ cells, and is highly conserved within mammals. While using semiquantitative PCR, we did not notice any difference in the C-KIT Band intensity among animals with different numBer of Bs (0-3). The presence of only one copy of C- KIT gene was confirmed using real time-PCR on genomic DNA of A. flavicollis specimens with different numBer of Bs. rRNA genes in eukaryotes’ genome are organized like units of tandem repeated sequences. The units form distinct clusters on one to several chromosome pairs. rRNA genes were found on Bs in different species including two species of genus Apodemus. One particular sample with 2 Bs showed the numBer of 18S rRNA gene aBout three times that of the caliBrator 0 B sample. This result can indicate the presence of 18S rRNA gene on Bs, But its confirmation requires the implementation of other methods. Still, we can neither confirm nor deny the existence of pseudogen of tested target genes, or lose of exon 1 of C-KIT protooncogen in Bs of A. flavicollis. Our findings are further discussed. [Projekat Ministarstva nauke RepuBlike SrBije, Br. 173003]

Vladimir A. Trifonov - One of the best experts on this subject based on the ideXlab platform.

  • Low-pass single-chromosome sequencing of human small supernumerary marker Chromosomes (sSMCs) and Apodemus B Chromosomes
    Chromosoma, 2018
    Co-Authors: Alexey I. Makunin, Marija Rajičić, Tatyana V. Karamysheva, Svetlana A. Romanenko, Anna S. Druzhkova, Nikolay B. Rubtsov, Alexander S. Graphodatsky, Mladen Vujosevic, Jelena Blagojevic, Vladimir A. Trifonov
    Abstract:

    Supernumerary Chromosomes sporadically arise in many eukaryotic species as a result of genomic rearrangements. If present in a suBstantial part of species population, those are called B Chromosomes, or Bs. This is the case for 70 mammalian species, most of which are rodents. In humans, the most common types of extra Chromosomes, sSMCs (small supernumerary marker Chromosomes), are diagnosed in approximately 1 of 2000 postnatal cases. Due to low frequency in population, human sSMCs are not considered B Chromosomes. Genetic content of Both B-Chromosomes and sSMCs in most cases remains understudied. Here, we apply microdissection of single Chromosomes with suBsequent low-pass sequencing on Ion Torrent PGM and Illumina MiSeq to identify unique and repetitive DNA sequences present in a single human sSMC and several B Chromosomes in mice Apodemus flavicollis and Apodemus peninsulae . The pipeline for sequencing data analysis was made availaBle in Galaxy interface as an addition to previously puBlished command-line version. Human sSMC was attriButed to the proximal part of chromosome 15 long arm, and Breakpoints leading to its formation were located into satellite DNA arrays. Genetic content of Apodemus B Chromosomes was species-specific, and minor alterations were oBserved in Both species. Common features of Bs in these Apodemus species were satellite DNA and ERV enrichment, as well as the presence of the vaccinia-related kinase gene Vrk1 . Understanding of the non-essential genome elements content provides important insights into genome evolution in general.

  • the origin of B Chromosomes in yellow necked mice apodemus flavicollis Break rules But keep playing the game
    PLOS ONE, 2017
    Co-Authors: Marija Rajicic, Tatyana V. Karamysheva, Svetlana A. Romanenko, Vladimir A. Trifonov, Jelena Blagojevic, Ivana Budinski, Tanja Adnađevic, A S Bogdanov, N B Rubtsov, Mladen Vujosevic
    Abstract:

    B Chromosomes (Bs) are known for more than hundred years But their origin, structure and pattern of evolution are not well understood. In the past few years new methodological approaches, involving isolation of Bs followed By whole DNA amplification, DNA proBe generation, and fluorescent in situ hyBridization (FISH) or the B chromosome DNA sequencing, has allowed detailed analysis of their origin and molecular structure in different species. In this study we explored the origin of Bs in the yellow-necked wood mouse, Apodemus flavicollis, using generation of microdissected DNA proBes followed By FISH on metaphase Chromosomes. Bs of A. flavicollis were successfully isolated and DNA was used as the template for B-specific proBes for the first time. We revealed homology of DNA derived from the analyzed B Chromosomes to the pericentromeric region (PR) of sex Chromosomes and suBtelomeric region of two pairs of small autosomes, But lower homology to the rest of the Y chromosome. Moreover, all analysed Bs had the same structure regardless of their numBer per individual or the great geographic distance Between examined populations from the Balkan Peninsula (SerBia) and Eastern Europe (south region of Russia and central Belarus). Therefore, it was suggested that B Chromosomes in A. flavicollis have a unique common origin from the PR of sex Chromosomes, and/or similar evolutionary pattern.

  • transcription of a protein coding gene on B Chromosomes of the siBerian roe deer capreolus pygargus
    BMC Biology, 2013
    Co-Authors: Vladimir A. Trifonov, Polina L Perelman, P V Dementyeva, Denis M Larkin, Patricia C M Obrien, Fengtang Yang, Malcolm A Fergusonsmith, Alexander S. Graphodatsky
    Abstract:

    Background: Most eukaryotic species represent staBle karyotypes with a particular diploid numBer. B Chromosomes are additional to standard karyotypes and may vary in size, numBer and morphology even Between cells of the same individual. For many years it was generally Believed that B Chromosomes found in some plant, animal and fungi species lacked active genes. Recently, molecular cytogenetic studies showed the presence of additional copies of protein-coding genes on B Chromosomes. However, the transcriptional activity of these genes remained elusive. We studied karyotypes of the SiBerian roe deer (Capreolus pygargus) that possess up to 14 B Chromosomes to investigate the presence and expression of genes on supernumerary Chromosomes. Results: Here, we descriBe a 2 MBp region homologous to cattle chromosome 3 and containing TNNI3K (partial), FPGT, LRRIQ3 and a large gene-sparse segment on B Chromosomes of the SiBerian roe deer. The presence of the copy of the autosomal region was demonstrated By B-specific cDNA analysis, PCR assisted mapping, cattle Bacterial artificial chromosome (BAC) clone localization and quantitative polymerase chain reaction (qPCR). By comparative analysis of B-specific and non-B chromosomal sequences we discovered some B chromosome-specific mutations in protein-coding genes, which further enaBled the detection of a FPGT-TNNI3K transcript expressed from duplicated genes located on B Chromosomes in roe deer fiBroBlasts. Conclusions: Discovery of a large autosomal segment in all B Chromosomes of the SiBerian roe deer further corroBorates the view of an autosomal origin for these elements. Detection of a B-derived transcript in fiBroBlasts implies that the protein coding sequences located on Bs are not fully inactivated. The origin, evolution and effect on host of B chromosomal genes seem to Be similar to autosomal segmental duplications, which reinforces the view that supernumerary chromosomal elements might play an important role in genome evolution.

  • Anchoring the dog to its relatives reveals new evolutionary Breakpoints across 11 species of the Canidae and provides new clues for the role of B Chromosomes
    Chromosome Research, 2011
    Co-Authors: Shannon E. Duke Becker, Alexander S. Graphodatsky, Vladimir A. Trifonov, Rachael Thomas, Robert K Wayne, Matthew Breen
    Abstract:

    The emergence of genome-integrated molecular cytogenetic resources allows for comprehensive comparative analysis of gross karyotype architecture across related species. The identification of evolutionarily conserved chromosome segment (ECCS) Boundaries provides deeper insight into the process of chromosome evolution associated with speciation. We evaluated the genome-wide distriBution and relative orientation of ECCSs in three wild canid species with diverse karyotypes (red fox, Chinese raccoon dog, and gray fox). Chromosome-specific panels of dog genome-integrated Bacterial artificial chromosome (BAC) clones spaced at ∼10-MB intervals were used in fluorescence in situ hyBridization analysis to construct integrated physical genome maps of these three species. Conserved evolutionary Breakpoint regions (EBRs) shared Between their karyotypes were refined across these and eight additional wild canid species using targeted BAC panels spaced at ∼1-MB intervals. Our findings suggest that the EBRs associated with speciation in the Canidae are compatiBle with recent phylogenetic groupings and provide evidence that these Breakpoints are also recurrently associated with spontaneous canine cancers. We identified several regions of domestic dog sequence that share homology with canid B Chromosomes, including additional cancer-associated genes, suggesting that these supernumerary elements may represent more than inert passengers within the cell. We propose that the complex karyotype rearrangements associated with speciation of the Canidae reflect unstaBle chromosome regions descriBed By the fragile Breakage model.

  • mapping of kit adjacent sequences on canid autosomes and B Chromosomes
    Cytogenetic and Genome Research, 2007
    Co-Authors: Dmitry V Yudkin, Vladimir A. Trifonov, Fengtang Yang, Malcolm A Fergusonsmith, Anna V Kukekova, N V Vorobieva, Nadezhda V Rubtsova, Gregory M Acland, Alexander S. Graphodatsky
    Abstract:

    B Chromosomes are often considered to Be one of the most mysterious elements of karyotypes (Camacho, 2004). It is generally Believed that mammalian B Chromosomes do not contain any protein coding gene

Cesar Martins - One of the best experts on this subject based on the ideXlab platform.

  • Article Origin and Evolution of B Chromosomes in the Cichlid Fish Astatotilapia latifasciata Based on Integrated Genomic Analyses
    2020
    Co-Authors: Guilherme T. Valente, B E A Fantinatti, Cesar Martins, Matthew A Conte, Robson Francisco Carvalho, Thomas D Kocher, Diogo C Cabral-de-mello, Marcelo R Vicari, Miriam Barlow
    Abstract:

    ABstract Approximately 15% of eukaryotes contain supernumerary B Chromosomes. When present, B Chromosomes frequently represent as much as 5% of the genome. Despite thousands of reports descriBing the distriBution of supernumeraries in various taxa, a comprehensive theory for the origin, maintenance, and evolution of B Chromosomes has not emerged. Here, we sequence the complete genomes of individual cichlid fish (Astatotilapia latifasciata) with and without B Chromosomes, as well as microdissected B Chromosomes, to identify DNA sequences on the B. B sequences were further analyzed through quantitative polymerase chain reaction and in situ hyBridization. We find that the B chromosome contains thousands of sequences duplicated from essentially every chromosome in the ancestral karyotype. Although most genes on the B chromosome are fragmented, a few are largely intact, and we detect evidence that at least three of them are transcriptionally active. We propose a model in which the B chromosome originated early in the evolutionary history of Lake Victoria cichlids from a small fragment of one autosome. DNA sequences originating from several autosomes, including protein-coding genes and transposaBle elements, suBsequently inserted into this proto-B. We propose that intact B chromosome genes involved with microtuBule organization, kinetochore structure, recomBination and progression through the cell cycle may play a role in driving the transmission of the B chromosome. Furthermore, our work suggests that karyotyping is an essential step prior to genome sequencing to avoid proBlems in genome assemBly and analytical Biases created By the presence of high copy numBer sequences on the B chromosome

  • The Modern View of B Chromosomes Under the Impact of High Scale Omics Analyses
    'MDPI AG', 2019
    Co-Authors: Syed Farhan Ahmad, Cesar Martins
    Abstract:

    Supernumerary B Chromosomes (Bs) are extra karyotype units in addition to A Chromosomes, and are found in some fungi and thousands of animals and plant species. Bs are uniquely characterized due to their non-Mendelian inheritance, and represent one of the Best examples of genomic conflict. Over the last decades, their genetic composition, function and evolution have remained an unresolved query, although a few successful attempts have Been made to address these phenomena. A classical concept Based on cytogenetics and genetics is that Bs are selfish and aBundant with DNA repeats and transposons, and in most cases, they do not carry any function. However, recently, the modern quantum development of high scale multi-omics techniques has shifted B research towards a new-Born field that we call “B-omics„. We review the recent literature and add novel perspectives to the B research, discussing the role of new technologies to understand the mechanistic perspectives of the molecular evolution and function of Bs. The modern view states that B Chromosomes are enriched with genes for many significant Biological functions, including But not limited to the interesting set of genes related to cell cycle and chromosome structure. Furthermore, the presence of B Chromosomes could favor genomic rearrangements and influence the nuclear environment affecting the function of other chromatin regions. We hypothesize that B Chromosomes might play a key function in driving their transmission and maintenance inside the cell, as well as offer an extra genomic compartment for evolution

  • the hnrnp q like gene is retroinserted into the B Chromosomes of the cichlid fish astatotilapia latifasciata
    Chromosome Research, 2017
    Co-Authors: Bianca De Oliveira Carmello, B E A Fantinatti, Erica Ramos, Guilherme T. Valente, Adauto Lima Cardoso, Rogério Antonio De Oliveira, Rafael Luiz Buogo Coan, D F Marques, Cesar Martins
    Abstract:

    B Chromosomes are dispensaBle elements oBserved in many eukaryotic species, including the African cichlid Astatotilapia latifasciata, which might have one or two B Chromosomes. Although there have Been many studies focused on the Biology of these Chromosomes, questions aBout the evolution, maintenance, and potential effects of these Chromosomes remain. Here, we identified a variant form of the hnRNP Q-like gene inserted into the B chromosome of A. latifasciata that is characterized By a high copy numBer and intron-less structure. The aBsence of introns and presence of transposaBle elements with a reverse transcriptase domain flanking hnRNP Q-like sequences suggest that this gene was retroinserted into the B chromosome. RNA-Seq analysis did not show that the B variant retroinserted copies are transcriptionally active. However, RT-qPCR results showed variations in the canonical hnRNP Q-like copy expression levels among exons, tissues, sex, and B presence/aBsence. Although the patterns of transcription are not well understood, the exons of the B retrocopies were overexpressed, and a Bias for female B+ expression was also oBserved. These results suggest that retroinsertion is an additional and important mechanism contriButing to B chromosome formation. Furthermore, these findings indicate a Bias towards female differential expression of B chromosome sequences, suggesting that B Chromosomes and sex determination are somehow associated in cichlids.

  • origin and evolution of B Chromosomes in the cichlid fish astatotilapia latifasciata Based on integrated genomic analyses
    Molecular Biology and Evolution, 2014
    Co-Authors: Guilherme T. Valente, Marcelo Ricardo Vicari, B E A Fantinatti, Matthew A Conte, Diogo Cavalcanti Cabraldemello, Robson Francisco Carvalho, Thomas D Kocher, Cesar Martins
    Abstract:

    Approximately 15% of eukaryotes contain supernumerary B Chromosomes. When present, B Chromosomes frequently represent as much as 5% of the genome. Despite thousands of reports descriBing the distriBution of supernumeraries in various taxa, a comprehensive theory for the origin, maintenance, and evolution of B Chromosomes has not emerged. Here, we sequence the complete genomes of individual cichlid fish (Astatotilapia latifasciata )w ith and without B Chromosomes, as well as microdissected B Chromosomes, to identify DNA sequences on the B. B sequences were further analyzed through quantitative polymerase chain reaction and in situ hyBridization. We find that the B chromosome contains thousands of sequences duplicated from essentiall ye very chromosome in the ancestral karyotype. Although most genes on the B chromosome are fragmented, a few are largely intact, and we detect evidence that at least three of them are transcriptionally active. We propose a model in which the B chromosome originated early in the evolutionary history of Lake Victoria cichlids from as mall fragment of one autosome. DNA sequences originating from several autosomes, including protein-coding genes and transposaBle elements, suBsequently inserted into this proto-B. We propose that intact B chromosome genes involved with microtuBule organization, kinetochore structure, recomBination and progression through the cell cycle may play a role in driving the transmission of the B chromosome. Furthermore, our work suggests that karyotyping is an essential step prior to genome sequencing to avoid proBlems in genome assemBly and analytical Biases created By the presence of high copy numBer sequences on the B chromosome.

  • the B Chromosomes of the african cichlid fish haplochromis oBliquidens harBour 18s rrna gene copies
    BMC Genetics, 2010
    Co-Authors: Andreia B Poletto, Irani A Ferreira, Cesar Martins
    Abstract:

    Diverse plant and animal species have B Chromosomes, also known as accessory, extra or supernumerary Chromosomes. Despite Being widely distriButed among different taxa, the genomic nature and genetic Behavior of B Chromosomes are still poorly understood. In this study we descriBe the occurrence of B Chromosomes in the African cichlid fish Haplochromis oBliquidens. One or two large B chromosome(s) occurring in 39.6% of the analyzed individuals (Both male and female) were identified. To Better characterize the karyotype and assess the nature of the B Chromosomes, fluorescence in situ hyBridization (FISH) was performed using proBes for telomeric DNA repeats, 18S and 5S rRNA genes, SATA centromeric satellites, and Bacterial artificial Chromosomes (BACs) enriched in repeated DNA sequences. The B Chromosomes are enriched in repeated DNAs, especially non-active 18S rRNA gene-like sequences. Our results suggest that the B chromosome could have originated from rDNA Bearing suBtelo/acrocentric A Chromosomes through formation of an isochromosome, or By accumulation of repeated DNAs and rRNA gene-like sequences in a small proto-B chromosome derived from the A complement.

Alexander S. Graphodatsky - One of the best experts on this subject based on the ideXlab platform.

  • Low-pass single-chromosome sequencing of human small supernumerary marker Chromosomes (sSMCs) and Apodemus B Chromosomes
    Chromosoma, 2018
    Co-Authors: Alexey I. Makunin, Marija Rajičić, Tatyana V. Karamysheva, Svetlana A. Romanenko, Anna S. Druzhkova, Nikolay B. Rubtsov, Alexander S. Graphodatsky, Mladen Vujosevic, Jelena Blagojevic, Vladimir A. Trifonov
    Abstract:

    Supernumerary Chromosomes sporadically arise in many eukaryotic species as a result of genomic rearrangements. If present in a suBstantial part of species population, those are called B Chromosomes, or Bs. This is the case for 70 mammalian species, most of which are rodents. In humans, the most common types of extra Chromosomes, sSMCs (small supernumerary marker Chromosomes), are diagnosed in approximately 1 of 2000 postnatal cases. Due to low frequency in population, human sSMCs are not considered B Chromosomes. Genetic content of Both B-Chromosomes and sSMCs in most cases remains understudied. Here, we apply microdissection of single Chromosomes with suBsequent low-pass sequencing on Ion Torrent PGM and Illumina MiSeq to identify unique and repetitive DNA sequences present in a single human sSMC and several B Chromosomes in mice Apodemus flavicollis and Apodemus peninsulae . The pipeline for sequencing data analysis was made availaBle in Galaxy interface as an addition to previously puBlished command-line version. Human sSMC was attriButed to the proximal part of chromosome 15 long arm, and Breakpoints leading to its formation were located into satellite DNA arrays. Genetic content of Apodemus B Chromosomes was species-specific, and minor alterations were oBserved in Both species. Common features of Bs in these Apodemus species were satellite DNA and ERV enrichment, as well as the presence of the vaccinia-related kinase gene Vrk1 . Understanding of the non-essential genome elements content provides important insights into genome evolution in general.

  • transcription of a protein coding gene on B Chromosomes of the siBerian roe deer capreolus pygargus
    BMC Biology, 2013
    Co-Authors: Vladimir A. Trifonov, Polina L Perelman, P V Dementyeva, Denis M Larkin, Patricia C M Obrien, Fengtang Yang, Malcolm A Fergusonsmith, Alexander S. Graphodatsky
    Abstract:

    Background: Most eukaryotic species represent staBle karyotypes with a particular diploid numBer. B Chromosomes are additional to standard karyotypes and may vary in size, numBer and morphology even Between cells of the same individual. For many years it was generally Believed that B Chromosomes found in some plant, animal and fungi species lacked active genes. Recently, molecular cytogenetic studies showed the presence of additional copies of protein-coding genes on B Chromosomes. However, the transcriptional activity of these genes remained elusive. We studied karyotypes of the SiBerian roe deer (Capreolus pygargus) that possess up to 14 B Chromosomes to investigate the presence and expression of genes on supernumerary Chromosomes. Results: Here, we descriBe a 2 MBp region homologous to cattle chromosome 3 and containing TNNI3K (partial), FPGT, LRRIQ3 and a large gene-sparse segment on B Chromosomes of the SiBerian roe deer. The presence of the copy of the autosomal region was demonstrated By B-specific cDNA analysis, PCR assisted mapping, cattle Bacterial artificial chromosome (BAC) clone localization and quantitative polymerase chain reaction (qPCR). By comparative analysis of B-specific and non-B chromosomal sequences we discovered some B chromosome-specific mutations in protein-coding genes, which further enaBled the detection of a FPGT-TNNI3K transcript expressed from duplicated genes located on B Chromosomes in roe deer fiBroBlasts. Conclusions: Discovery of a large autosomal segment in all B Chromosomes of the SiBerian roe deer further corroBorates the view of an autosomal origin for these elements. Detection of a B-derived transcript in fiBroBlasts implies that the protein coding sequences located on Bs are not fully inactivated. The origin, evolution and effect on host of B chromosomal genes seem to Be similar to autosomal segmental duplications, which reinforces the view that supernumerary chromosomal elements might play an important role in genome evolution.

  • Anchoring the dog to its relatives reveals new evolutionary Breakpoints across 11 species of the Canidae and provides new clues for the role of B Chromosomes
    Chromosome Research, 2011
    Co-Authors: Shannon E. Duke Becker, Alexander S. Graphodatsky, Vladimir A. Trifonov, Rachael Thomas, Robert K Wayne, Matthew Breen
    Abstract:

    The emergence of genome-integrated molecular cytogenetic resources allows for comprehensive comparative analysis of gross karyotype architecture across related species. The identification of evolutionarily conserved chromosome segment (ECCS) Boundaries provides deeper insight into the process of chromosome evolution associated with speciation. We evaluated the genome-wide distriBution and relative orientation of ECCSs in three wild canid species with diverse karyotypes (red fox, Chinese raccoon dog, and gray fox). Chromosome-specific panels of dog genome-integrated Bacterial artificial chromosome (BAC) clones spaced at ∼10-MB intervals were used in fluorescence in situ hyBridization analysis to construct integrated physical genome maps of these three species. Conserved evolutionary Breakpoint regions (EBRs) shared Between their karyotypes were refined across these and eight additional wild canid species using targeted BAC panels spaced at ∼1-MB intervals. Our findings suggest that the EBRs associated with speciation in the Canidae are compatiBle with recent phylogenetic groupings and provide evidence that these Breakpoints are also recurrently associated with spontaneous canine cancers. We identified several regions of domestic dog sequence that share homology with canid B Chromosomes, including additional cancer-associated genes, suggesting that these supernumerary elements may represent more than inert passengers within the cell. We propose that the complex karyotype rearrangements associated with speciation of the Canidae reflect unstaBle chromosome regions descriBed By the fragile Breakage model.

  • mapping of kit adjacent sequences on canid autosomes and B Chromosomes
    Cytogenetic and Genome Research, 2007
    Co-Authors: Dmitry V Yudkin, Vladimir A. Trifonov, Fengtang Yang, Malcolm A Fergusonsmith, Anna V Kukekova, N V Vorobieva, Nadezhda V Rubtsova, Gregory M Acland, Alexander S. Graphodatsky
    Abstract:

    B Chromosomes are often considered to Be one of the most mysterious elements of karyotypes (Camacho, 2004). It is generally Believed that mammalian B Chromosomes do not contain any protein coding gene

  • the proto oncogene c kit maps to canid B Chromosomes
    Chromosome Research, 2005
    Co-Authors: Alexander S. Graphodatsky, Vladimir A. Trifonov, Polina L Perelman, Anna V Kukekova, Dmitry V Yudkin, N V Vorobieva, Violetta R Beklemisheva, Daria Graphodatskaya, Lyudmila N Trut, Fengtang Yang
    Abstract:

    Plant and animal karyotypes sometimes contain variaBle elements, that are referred to as additional or B-Chromosomes. It is generally Believed that B-Chromosomes lack major genes and represent parasitic and selfish elements of a genome. Here we report, for the first time, the localization of a gene to B-Chromosomes of mammals: red fox (Vulpes vulpes) and two suBspecies of raccoon dog (Nyctereutes procyonoides). Identification of the proto-oncogene C-KIT on B-Chromosomes of two Canidae species that diverged from a common ancestor more than 12.5 million years ago argues against the current view of B-Chromosomes. Analyses of fox B-chromosomal C-KIT gene from a flow-sorted fox B-chromosome-specific liBrary revealed the presence of intron-exon Boundaries and high identity Between sequenced regions of canine and fox B-chromosomal C-KIT copies. Identification of C-KIT gene on all B-Chromosomes of two canid species provides new insight into the origin and evolution of supernumeraries and their potential role in the genome.